In this study we utilize two organic geochemical proxies, the U37k′ index and TEX86, to examine past sea surface temperatures (SST) from a site located near the Nile River Delta in the eastern Mediterranean (EM) Sea. The U37k′ and TEX86 records generally are in agreement and indicate SST ranges of 14°C–26°C and 14°C–28°C, respectively, during the last 27 cal ka. During the Holocene, TEX86-based SST estimates are usually higher than U37k′-based SST estimates, which is likely due to seasonal differences between the timing of the haptophyte and crenarchaeota blooms in the EM and is related to the onset of the modern flow regime of the Nile River. Both records show that SST varied on centennial to millennial timescales in response to global climate events, i.e., cooling during the Last Glacial Maximum (LGM), Heinrich event 1 (H1), and the Younger Dryas (YD) and warming during the Bølling-Allerød and in the early Holocene during deposition of sapropel S1. The H1 cooling was particularly severe and is marked by a drop in SST of ∼4.5°C in comparison to pre-H1 SST, with temperatures >1°C cooler than during the LGM. In contrast to high-latitude and western Mediterranean records, which indicate both an abrupt onset and termination of the YD event, the transition from the YD to the Holocene was much more gradual in the EM.